Locus 4540

Sequence ID 2L_DroMel_CAF1
Location 12,999,393 – 12,999,489
Length 96
Max. P 0.694978
window7155 window7156

overview

Window 5

Location 12,999,393 – 12,999,489
Length 96
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 94.38
Mean single sequence MFE -26.98
Consensus MFE -23.42
Energy contribution -23.70
Covariance contribution 0.28
Combinations/Pair 1.12
Mean z-score -1.31
Structure conservation index 0.87
SVM decision value 0.34
SVM RNA-class probability 0.694978
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12999393 96 + 22407834
AGAAAAAGGCACUGGGCCGCAACCGGGACAGGAUCCGGGGAAAAUGCGUAAAAGCAAAGCAGGAAUUACGCGGCGGGUAGAGUAAUUGUCCGGGCA
........((.(((((((((..(((((......)))))......(((......))).............))))).....((....))..)))))). ( -28.20)
>DroSec_CAF1 24613 96 + 1
AGAAAAAGGCACUGGGACGCAACCGGGACAGGAUCCGGGGAAAAUGCGUAAAGGCAAAGCAGGAAUUACGCGGCGGGUGGAGUAAUUGUCCGGGCA
........((.((...(((((.((.(((.....))).)).....)))))..))))...((.((((((((.(.(....).).)))))..)))..)). ( -25.90)
>DroSim_CAF1 23517 96 + 1
AGAAAAAGGCACUGGGCCGCAACCGGGACAGGAUCCGGGGAAAAUGCGUAAAGGCAAAGCAGGAAUUACGCGGCGGGUGGAGUAAUUGUCCGGGCA
........((.(((((((((..(((((......)))))......(((((((..((...)).....)))))))))))...((....)).))))))). ( -28.40)
>DroEre_CAF1 26249 96 + 1
AGAAAAAGGCACCGGUCCGCGACCGGAACAGGGACCGGGGAAAAUGCGUAAAGGCAAAGCAGGAAUUACGCGGCGGGUGGAGUAAUUGUCUGGGCA
.........((((.(.(((((.((((........))))......(((......)))............)))))).)))).......(((....))) ( -27.60)
>DroYak_CAF1 23670 96 + 1
AGAAAAAGGCACUGGGCCACAACCGGAACAGGGUCCGGGGAAAAUGCGUAAAGGCAAAGGAGGAAUUACGCGGCGGGUGGAGUAAUUGUCUGGGCA
........((.(..((((((..(((((......)))))......(((((((...(.......)..)))))))....)))((....)))))..))). ( -24.80)
>consensus
AGAAAAAGGCACUGGGCCGCAACCGGGACAGGAUCCGGGGAAAAUGCGUAAAGGCAAAGCAGGAAUUACGCGGCGGGUGGAGUAAUUGUCCGGGCA
........((.((((((.((..(((((......)))))......(((......)))..))...((((((.(.(....).).)))))))))))))). (-23.42 = -23.70 +   0.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,999,393 – 12,999,489
Length 96
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 94.38
Mean single sequence MFE -20.98
Consensus MFE -19.22
Energy contribution -18.86
Covariance contribution -0.36
Combinations/Pair 1.12
Mean z-score -1.17
Structure conservation index 0.92
SVM decision value 0.28
SVM RNA-class probability 0.666122
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12999393 96 - 22407834
UGCCCGGACAAUUACUCUACCCGCCGCGUAAUUCCUGCUUUGCUUUUACGCAUUUUCCCCGGAUCCUGUCCCGGUUGCGGCCCAGUGCCUUUUUCU
.(((.(((((...............((((((.....((...))..))))))....((....))...))))).)))...(((.....)))....... ( -21.30)
>DroSec_CAF1 24613 96 - 1
UGCCCGGACAAUUACUCCACCCGCCGCGUAAUUCCUGCUUUGCCUUUACGCAUUUUCCCCGGAUCCUGUCCCGGUUGCGUCCCAGUGCCUUUUUCU
.((..((((................((((((...(......)...)))))).......((((........))))....))))..)).......... ( -19.40)
>DroSim_CAF1 23517 96 - 1
UGCCCGGACAAUUACUCCACCCGCCGCGUAAUUCCUGCUUUGCCUUUACGCAUUUUCCCCGGAUCCUGUCCCGGUUGCGGCCCAGUGCCUUUUUCU
.((.((((.......)))..((((.((((((...(......)...)))))).......((((........))))..))))....).))........ ( -21.60)
>DroEre_CAF1 26249 96 - 1
UGCCCAGACAAUUACUCCACCCGCCGCGUAAUUCCUGCUUUGCCUUUACGCAUUUUCCCCGGUCCCUGUUCCGGUCGCGGACCGGUGCCUUUUUCU
.................((((.((((((............(((......)))......((((........)))).))))).).))))......... ( -22.20)
>DroYak_CAF1 23670 96 - 1
UGCCCAGACAAUUACUCCACCCGCCGCGUAAUUCCUCCUUUGCCUUUACGCAUUUUCCCCGGACCCUGUUCCGGUUGUGGCCCAGUGCCUUUUUCU
.................(((..(((((((((...(......)...)))))).......(((((......)))))....)))...)))......... ( -20.40)
>consensus
UGCCCGGACAAUUACUCCACCCGCCGCGUAAUUCCUGCUUUGCCUUUACGCAUUUUCCCCGGAUCCUGUCCCGGUUGCGGCCCAGUGCCUUUUUCU
.....(((.((.((((....((((.((((((...(......)...)))))).......((((........))))..))))...))))...)).))) (-19.22 = -18.86 +  -0.36)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:34 2006